Team:SYSU-Software/Proof Of Concept
Proof of Concept
To reflect our project as a prototype to implement automated top-down genetic circuit design, we demonstrate how our software works in the following videos.
TRY Maloadis!
Design, simulate, save
Create a new file on maloadis
you can choose mannual design to draw a new circuit by yourself.
Draw a genetic circuit design
On the panel to the right of the canvas, you can search for parts, or create parts of your own, and drag them in to draw a design.
You can link parts together to mark their interaction relationships (stimulate or inhibit).
Simulate the expression of a genetic circuit
Click simulation. Enter parameters and click start. You can get a simulation of how the concentration of the target changes with time shown in a graph, the x axis represting time/h and the y axis representing concetration/μM.
Save your design
Click “save” on the top left and your design will be exported in txt which can be opened again. Meanwhile, your designed will be saved in our database.
Image search in iGEM Registry
Draw or open an image on your design canvas. You can choose to search for elements (part inforamtion) and/or match structures. When most of your parts are from iGEM Registry, your image will be searched in iGEM Registry. You can click on the link to view full result.
Image search in ACS database
When most of your parts are non-standardize parts outside iGEM Registry, your image will be searched in ACS database. You can click on the link to view the article.
Automated design
Click "GeneNet Automation" on the top. Enter your parameters (for more detail information see our genenet page), click start. You will get a matrix of GeneNet Algorithm's result. Click process, and you will get a deigned genetic circuit on your canvas.
Bayesian Optimization
Click “Bayes Optimization”. Enter Number of iterations and number of genes.
In the demo, we used a 2-gene model. The function describing the relationship between the yield (express score, z) and the expression level of the 2 genes (x, y) is:
z = x2 - y2
Bayesian Optimization returns the recommended expression level of the 2 genes for the first round. Type in the result of z calculated with these expression level, click “process” and Bayesian Optimization will return another set of expression level. Input the new z in the express score and click “process” again. With our input (representing experimental result), the program renews the distribution of the function and finds the current possible global optimal solution after every iteration round.
Combining metabolic design and genetic circuit design together
When you open Maloadis, you will see a pop-up window which briefly describes Tongji-Software’s Synthesis Navigator.
Click “learn more”, and users will be linked to a page describing the function of Synthesis Navigator.
Click “visit their website” and users will be linked to https://www.tjigem.com/ to start using Synthesis Navigator.